We present a high precision particle-by-particle 3D reconstruction of granular systems composed of monodispersed spheres (sphere packings); the experimental approach is based on magnetic resonance imaging techniques. Our measurements revealed a strong correlation between the volume defined by the distance to the first nearest neighbor and the long-range average density. The main contribution to the amplitude decay of the correlation function can be described as exponential rather than power law up to a range equal to 7 sphere diameters. No evidence of geometrical structural changes as a function of the density was observed and neither regular crystallites nor any other statistically significant structures could be ascribed to a specific local arrangement. We concluded that granular compaction is the result of a process through which the system changes the average size of local structures without changing their local geometrical characteristics. These conclusions are supported by two-body correlation functions and Voronoi polyhedra space decomposition. The results provide a different perspective on the mechanisms underlying compaction with respect to previous works, and allow to discriminate between the different existing theoretical approaches.